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Conserved domains on  [gi|515741985|ref|WP_017174585|]
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MULTISPECIES: putative DNA-binding protein [Staphylococcus]

Protein Classification

YlxM family DNA-binding protein( domain architecture ID 10011255)

YlxM family DNA-binding protein similar to Bacillus subtilis UPF0122 family protein YlxM

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 6-109 8.52e-43

putative DNA-binding protein; Validated


:

Pssm-ID: 234647  Cd Length: 104  Bit Score: 135.37  E-value: 8.52e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985   6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 515741985  86 YNEMKQSIHDTKKLEHLIQKLEEL 109
Cdd:PRK00118  81 FDKIAYLKEKYPDDEELKKLIEIL 104
 
Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 6-109 8.52e-43

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 135.37  E-value: 8.52e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985   6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 515741985  86 YNEMKQSIHDTKKLEHLIQKLEEL 109
Cdd:PRK00118  81 FDKIAYLKEKYPDDEELKKLIEIL 104
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
6-110 1.51e-41

Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];


Pssm-ID: 442041  Cd Length: 112  Bit Score: 132.59  E-value: 1.51e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985   6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQKL 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 515741985  86 YNEMKQSIHDT------KKLEHLIQKLEELE 110
Cdd:COG2739   81 LEEIKELLEELeeseddEELEKLIEELEELE 111
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 6-103 2.46e-33

Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.


Pssm-ID: 282193  Cd Length: 98  Bit Score: 111.32  E-value: 2.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985    6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNEL 80

                          90
                  ....*....|....*...
gi 515741985   86 YNEMKQSIHDTKKLEHLI 103
Cdd:pfam04297  81 YDKIKDHQLRDKQLIEKI 98
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 23-61 1.83e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 35.79  E-value: 1.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 515741985   23 LTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRR 61
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKR 149
 
Name Accession Description Interval E-value
PRK00118 PRK00118
putative DNA-binding protein; Validated
 6-109 8.52e-43

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 135.37  E-value: 8.52e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985   6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:PRK00118   1 LEKTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNEL 80

                         90       100
                 ....*....|....*....|....
gi 515741985  86 YNEMKQSIHDTKKLEHLIQKLEEL 109
Cdd:PRK00118  81 FDKIAYLKEKYPDDEELKKLIEIL 104
YlxM COG2739
Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];
6-110 1.51e-41

Predicted DNA-binding protein YlxM, UPF0122 family [Transcription];


Pssm-ID: 442041  Cd Length: 112  Bit Score: 132.59  E-value: 1.51e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985   6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:COG2739    1 LEKTVRINLLFDFYGELLTEKQREYLELYYNDDLSLGEIAEELGISRQAVYDNIKRAEKILEEYEEKLGLVEKFQKRQKL 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 515741985  86 YNEMKQSIHDT------KKLEHLIQKLEELE 110
Cdd:COG2739   81 LEEIKELLEELeeseddEELEKLIEELEELE 111
UPF0122 pfam04297
Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to ...
 6-103 2.46e-33

Putative helix-turn-helix protein, YlxM / p13 like; Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.


Pssm-ID: 282193  Cd Length: 98  Bit Score: 111.32  E-value: 2.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515741985    6 LVKTLRMNYLFDFYHSLLTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRRTGDLVEDYETKLKLYEKFEQRQMI 85
Cdd:pfam04297   1 LEKTLRMNYLFDFYQSLLTDKQRNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKILEDYEKKLHLYEKYKLRNEL 80

                          90
                  ....*....|....*...
gi 515741985   86 YNEMKQSIHDTKKLEHLI 103
Cdd:pfam04297  81 YDKIKDHQLRDKQLIEKI 98
COG1356 COG1356
Transcriptional regulator [Transcription];
15-71 7.20e-04

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 36.37  E-value: 7.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515741985  15 LFDFYHSLLTEKQKNYLELfYLNDYSLSEIAETFKVSRQAV-------YDNIRRTGDLVEDYET 71
Cdd:COG1356    1 MFDAKYSLLTRRQAEVLAL-RERGLTQQEIADILGTSRANVssieksaRENIEKARETLAFYET 63
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 23-61 1.16e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 36.51  E-value: 1.16e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 515741985  23 LTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRR 61
Cdd:COG1595  128 LPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSR 166
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 23-61 1.83e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 35.79  E-value: 1.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 515741985   23 LTEKQKNYLELFYLNDYSLSEIAETFKVSRQAVYDNIRR 61
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKR 149
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 23-55 2.08e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 33.56  E-value: 2.08e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 515741985   23 LTEKQKNYLELFYLNDYSLSEIAETFKVSRQAV 55
Cdd:pfam04545   5 LPPRERQVLVLRYGEGLTLEEIGERLGISRERV 37
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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